Pretty_html
Leilynaz Malekafzali (33305137)
version April 25, 2018
- R Markdown PDF Challenge
- Module 1:
- Evidence Worksheet for “Prokaryotes: The Unseen Majority”
- Evidence Worksheet_02 “Life and the Evolution of Earth’s Atmosphere”
- Evidence Worksheet_ 03 “The Anthropocene”
- Problem set_01 for “Prokaryotes: The Unseen Majority”
- Problem set_02 “Microbial Engines”
- Writing Assignment 1
- Screen shots from marked module 1 essay
- Module 1 References:
- Module 2:
- Module 3:
R Markdown PDF Challenge
The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.
http://phdcomics.com/ Comic posted 1-17-2018
Challenge Goals
The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
hint: go to the PhD Comics website to see if you can find the image above
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown
Here’s a header!
Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).
Another header, now with maths
Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:
1231521+12341556280987## [1] 1.234156e+13Table Time
Or maybe, after you’ve added those numbers, you feel like it’s about time for a table!
I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the future.
library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")| speed | dist | |
|---|---|---|
| Min. : 4.0 | Min. : 2.00 | |
| 1st Qu.:12.0 | 1st Qu.: 26.00 | |
| Median :15.0 | Median : 36.00 | |
| Mean :15.4 | Mean : 42.98 | |
| 3rd Qu.:19.0 | 3rd Qu.: 56.00 | |
| Max. :25.0 | Max. :120.00 |
And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!
Module 1:
Evidence Worksheet for “Prokaryotes: The Unseen Majority”
Learning Objectives
Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
General Questions
What were the main questions being asked?
What is the number of prokaryotic cells in different environments on Earth? Which areas are the prokaryotes the most abundant? What is the amount of prokaryotic cellular carbon in different habitats? How much of the total Earth carbon content is contributed by the prokaryotic cellular carbon? What is the turn over rate of the prokaryotic population and how does it contribute to the mutation rate and therefore diversity in prokaryotes?
What were the primary methodological approaches used?
The primary methodological approaches are estimations which is to take small samples to represent the habitat. Additionally, they use the cell density, volume, and cellular carbon of prokaryotes to calculate total number of cells in a habitat. Specific calculation of each habitat methodological approaches: For aquatic environment (polar region)- they estimated number of prokaryotes based on the mean cell numbers reported in previous literature Delille and Rosiers, and the mean areal extent of seasonal ice. For soil- they estimated the number of prokaryotes based on detained direct counts from a coniferous forest ultisol. They used this estimate and applied it to all the forest soils. For subsurface- they used few direct enumerationd of subsurface prokaryotes. For deeper sediments, they extrapolated the number of prokaryoted based on a formula. Another approach that they used is based on the porosity of the terrestrial subsurface, and total pore space occupied by prokaryotes. Also they used the number of unattached prokaryoted calculated from groundwater data from previous studies. To calculate Carbon content- They used the prokaryotic cell numbers, and then they assumed that the amount of the cellular carbon is half of the dry weight. They also assumed the amount of carbon production should be 4 times the the carbon content based on the efficiency of carbon assimilation. They used this information to make an assumption about the turn over rate of prokaryotes.
Summarize the main results or findings.
Most of the prokaryotes reside in open ocean (1.2 x 10^29), soil (1.2 x 10^29), oceanic (3.5 x 10^30) and terrestrial subsurfaces (0.25-2.5 x 10^30). The number of prokaryotes on Earth is estimated to be 4-6 x 10^30 cells. The amount of prokaryotic cellular carbon on Earth is estimated to be 350-550 Pg. Including prokaryotic carbon in global models will nearly double the amount of carbon stored in living organisms.Prokaryotes contain 85-130 Pg of N and 9-14 Pg of P, which is about 10-fold more nutrients than found in plants.The average turn over times of prokaryotes is 6-25 days in the upper 200 m of the open ocean, 0.8 yr in the ocean below 200 m, 2.5 yr in soil, and 1-2 x 10^3 yr in subsurface. The cellular production rate for prokaryotes is estimated to be 1.7 x 10^30 cells/year.Prokaryotes exist in plants, air, and leafs but the number is much lower compared to the large resivors. Due to the abundance of prokaryotes and high turn over rates, there is an enormous genetic diversity among prokaryotes.
Do new questions arise from the results?
How do we define prokaryotes? what is the composition of microbes in each compartment? What are the measures that have to be taken into account in the phylogenic analyses to distinguish prokaryotes from eukaroytes? Is there any better measuring techniques in place that can lower the assumptions and error? How reliable are the numbers that are mentioned in this article? How does the turn over rate of the prokaryotes affect the nutrient cycles and impact other organisms?
Evidence Worksheet_02 “Life and the Evolution of Earth’s Atmosphere”
Learning objectives:
Comment on the emergence of microbial life and the evolution of Earth systems
General Questions
Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.
4.6 billion years ago : Inner planets received carbon and water vapour. star system developed due to super nova explotions. Moon formed and spin and tilt of Earth evolved leading to present day and night cycles and seasons.
4.5-4.1 billion years ago: Due to early sun being weak, high levels of CO2 increased the temperature.
4.2 billion years ago : Evidence of life (Isotopes of C preserved in grafite). Oldest Rock (Coherent assamblages of mineral).
3.8 billion years ago : Oldest sedimentary rocks and methanogenesis- oceans and weathering- maybe the oldest known sediments.
3.5 billion years ago : Photosynthesis by Cyanobacteria and microfossils and stromatolites present. Stromatolites are organosedimentary structures produced by microbial trapping.
2.7 billion years ago : Great oxidation event: responsible for glaciation. Here the planet would have been brown because of the methanogens to keep the planet warm because the sun was less illuminant.
2.2 billion years ago : Increase in biological production.
1.7 billion years ago : Appearance of eukaryotes in the form of algea.
1.1 billion years ago : Snowball Earth
550,000 years ago : Cambrian explosion where larger animals appear. Land plants also observed which once again increase the oxygen concentration in atmosphere.
200,000 years ago : Gigantic organims appear. Permian extinction when 95% of species extinct.
Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:
Hadean : During this time, there was a high concentration of CO2 to keep the Earth warm as the sun was 30% less illuminant. Earth was also very hot. Spin and tilt of the Earth evolved due to the formation of moon. Star system formed due to super nova explosion.
Archean : High concentration of methane produced by methanogens to keep th Earth warm. Some O2 was present in the atmosphere due to the photosynthesis of Cyanobacteria.
Proterozoic : CO2 produced as a result of the raction between oxygen and methane. This was responsible for making the Earth cold due to the decrease in the green house effect which lead to glaciation.
Phanerozoic : Increase in atmospheric oxygen concentration due to increase in land plants. Formation of coal deposits die to the death of the organims.
Evidence Worksheet_ 03 “The Anthropocene”
Learning Objectives
Evaluate human impacts on the ecology and biogeochemistry of Earth systems.
Specific questions
What were the main questions being asked?
How humans can operate safely and prevent their activities to cause environmental changes? What is the threshold within which humans should operate? How can boundaries for various processes be combined and connected? How have humans impacted Earth?
What were the primary methodological approaches used?
The author develops his arguments through citing multiple authors and books in the paper. Using Planetary boundaries. For defining these boundaries, the author cite various literatures on the fossil records about the extinction rates and atmospheric carbon dioxide levels.
Summarize the main results or findings.
Unacceptable environmental changes can be generated if the threshold is crossed for the processes. 9 processes were discussed that need planetary boundaries: change in land use, atmospheric aerosol loading, ocean acidification, global fresh water use, stratospheric ozone depletion, rate of biodiversity loss, climate change, and interference with nitrogen and phosphorus cycles. Some of the boundaries for these processes have been passed such as for climate change. Additionally, the boundaries for some other processes are soon to be approached such as global freshwater use. If these thresholds are not crossed by humans, they can purse long-term social and economic developments. Changes in the atmospheric carbon dioxide should not exceed 350 parts per million by volume.
Do new questions arise from the results?
Are the proposed models for setting boundaries reliable? Are the threshold discussed take into account the increasing rate of human activities on Earth? Does these threshold values vary from location to location on Earth?
Problem set_01 for “Prokaryotes: The Unseen Majority”
Learning objective
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
Specific questions
What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.
It has been indicated that most of the prokaryotes reside in three large habitats: seawater, soil and the sediment/soil subsurface. Aquatic- 1.181 x 10^29 cells. Soil- 2.556 x 10^29. Subsurface sediments- 3.8 x 10^30 (oceanic subsurface: 3.5 x 10^30 and terrestrial subsurface: 0.25-2.5 x 10^30).
What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?
The estimated prokaryotic cell abundance is 3.6 x 10^28 in the upper 200 m at cellular density of 5 x 10^5 cells/ml. The average cellular density of the autotrophic marine. cyanobacteria and prochlorococcus spp. in the upper 200 m is 4 x 10^4 cells/ml. The fraction is : (4x 10^4)/ (5x 10^5) = 8%. This means that 8% of the autotrophic prokaryotes in charge of carbon cycle in the ocean to provide organic carbon for the majority of the hetrotrophic prokaryotes.
What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
Autotrophs is “self- nourishing”, fix inorganic carbon (CO2) into biomass using light source as energy. Heterotroph: assimilate organic carbon- Uses organic substrates for both Carbon and energy source. Litotroph: use inorganic substrates for C source and energy source.
Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
Subsurface: Teressterial and marine: ~4 Km deep in the subsurface there is life. Deepest point in the ocean is Mariana’s Trench: 10.9 km down. Therefore 4 km lower than Mariana’s Trech is 14.9 km deep down that life could exist.Temperature is the limiting factor- it is about 125 C. Change in temperature is 22 C/km.
Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
Mount Everst is the highest point which is about 8.8 km above the sea level. Also microbes have been found to be transported up to 77 km. However the limiting factor is the ionizing radiation and lack of nutrients and moisture. Therefore the microbes might not be metabolizing and maybe spores.
Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
From the top of mount Everest (8.8 km up) to the bottom of Mariana’s Trench (10.9 km down) and 4 km deeper in to the sediment is 24 km.
How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
Population x turn overtime /year Ex. for marine habitats: (3.6 x 10^28 cells x 365 days/ 16 turnover = 8.2 x 10^29 cells/ yr)
What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
Carbon efficiency- assumed to be 20%- only this percent is being assimilated. About 5-20 fg on average C in prokaryotic cells (used 20 fg for calculations): About 20 x 10^-30 pg/ cell.
3.6 x 10^ 28 cells x 20 x10^-30 pg/ cell = 0.72 pg carbon in marine heterotrophs.
They used multiplier of 4 instead of 5 for 20%-> 4 x 0,72= 2.88 pg/ yr.
51 pg/ yr (carbon in photic zone) x 85% consumed = 43 pg C
43 pg C/ yr / 2.88 pg /yr = 14.9 or 1 turnover every 24.5 days. Half of the carbon of the planet is among the prokaryotes. This number vary with depth in ocean and between terrestrial and marine habitats due to the change in microbial population.
Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
Mutations in prokaryotic cells are the major source of diversity and one of the essential factors in the formation of novel species. Additionally, due to mutations, prokaryotes can be selected for and adapt to variety of environments. Point mutations are not the only way in which microbial genomes diversify and adapt. Horizontal gene transfer (HGT), insertions, deletions, and vertical gene transfer are other ways that microbial genome can diversity and adapt.
What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?
Large population size and rapid replication of prokaryotes implies that extremely rare events can occur frequently. High mutation leads to increase in diversity and therefore increase in metabolic potential in response to stress and selective pressure.
Problem set_02 “Microbial Engines”
Learning objectives:
Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles.
Specific Questions:
What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?
Geophysical: Tectonics and atmospheric photochemical processes-> supply substrates and remove products. They allow elements and molecules to interact with each other, and chemical bonds to form and break in cyclical manner.
Biogeochemical: The biological fluxes of 6 major elements- H,C,N,O,S, and P that constitute major building blocks for all biological macromolecules. Geochemical reactions are based on acid/ base chemistry. The biogeochemical fluxes are driven largely by microbes that catalyze thermodynamically constrained reactions. Additionally, volcanism and rock weathering play a role in resupply of C, S, and P.
Abiotic reactions: are based on acid/base chemistry (transfer of protons without electrons).
Biotic reactions: redox reaction that is dependant on the successive transfers of electrons and protons from a relatively limited set of chemical elements.
The way that the biotic and abotic processes are interconnected is that biogeochemical cycles have evolved on a planetary scale to form a set of nested abiotiotically driven acid/base reactions and biologically driven redox reactions that set lower limits on external energy that are required to sustain these cycles.
Why is Earth’s redox state considered an emergent property?
This is because feedbacks between the evolution of microbial metabolic and geochemical processes create the average redox condition of the oceans and atmosphere. Therefore, Earth’s redox state is an emergent property of microbial life on a planetary scale.
How do reversible electron transfer reactions give rise to element and nutrient cycles at different ecological scales? What strategies do microbes use to overcome thermodynamic barriers to reversible electron flow?
Microbes carry genes that encode the multimerci protein complexes (machinery) responsible for redox chemistry (transfers of electron and protons) half-cells that form the basis of the major energy transducting pathways. In order to overcome thermodynamic barriers to reversible electron flow, microbes use identical or near-identical pathways for forward and reverse reactions to maintain cycles. That in one direction the process is oxidative, dissimilatory and energy producing, and in the other direction it is reductive, assimilatory and energy consuming. This process requires the synergistic cooperation of multispecies assemblages, a phenomenon that is typical for most biogeochemical transformations.
Using information provided in the text, describe how the nitrogen cycle partitions between different redox “niches” and microbial groups. Is there a relationship between the nitrogen cycle and climate change?
For N2 to become accessible and be used in the synthesis of nucleic acids and proteins, N2 should be changed to NH4+ via nitrogen fixation. However, the enzyme responsible for fixation is inhibited by Oxygen. In the presence of oxygen, NH4+ can be oxidized to nitrate in a two-stage pathway, initially requiring a specific group of Bacteria or archea that oxidize ammonia to NO2- (via hydroxyamine), which is subsequently oxidized to NO3- by a different suite of nitrifying bacteria. The small differences in redox potential in the redox reactions is used by nitrifiers to reduce CO2 to organic matter. Finally, in the absence of oxygen, a third set of opportunistic microbes uses NO2- and NO3- as electron acceptors in anaerobic oxidation of organic matter. This pathway will ultimately form N2.
The major cuase of climate change is the green house effect due to increase in the concentration of green house gasses in the Earth’s atmosphere such as CO2. The nitrogen cycle affects the climate change, as CO2 is reduced to organic matter by the oxidation of NH4+ to NO2 and NO2 to NO3. Therefore this reduces atmospherinc CO2.
What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes?
The more diverse that the microbial community is, the more diverse are the metabolic activities that are observed in the community. The number of new protein families found are increasing linearly with the number of new genome sequenced. Also the discovery rate for new proteins is linearly even when the known number of protein sequences is increased threefold. This indicates that the journey of cataloguing extant protein sequence space is relatively new due to the limitless evolutionary diversity in nature.
Writing Assignment 1
Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides." Do you agree or disagree with this statement? Answer the question using specific reference to your reading, discussions and content from evidence worksheets and problem sets.
Microorganism, although invisible to the naked eye, are ubiquitous. They are the earliest inhabitants of the Earth and have evolved over the time to adapt to the ever-changing conditions on Earth. While humans are exploiting the resources on Earth and are contributing to its degradation, microbes are playing an extremely important role in the environmental transformations to make Earth a suitable place for humans. It can be reasonably argued that microbial life can easily live without humans, but humans cannot survive without the global catalysis and environmental transformation of microbes. In order to address this topic, it is important to discuss the dependency of the humans to the reactions catalysed by microbes, the role of microbes in reversing the negative effects that have been caused by humans on Earth, and the ability of microbes to adapt to various environments due to their high abundance and rapid growth rate.
Firstly, microbes play an essential role in catalyzing major biogeochemical fluxes of H, C, N, O, and S that humans cannot mimic it but depend on it for survival. These fluxes are made up of thermodynamically constrained redox reactions (1). In order to make these redox processes thermodynamically favorable, there is a requirement for the synergistic cooperation of multispecies assemblages (1). Therefore, microbes in a community cooperate by catalyzing coupled forward and reverse reactions, where one is oxidative and dissimilatory and the other is reductive and assimilatory (1). Since these metabolic pathways are coupled, the biosphere can approach self-sustaining element cycling (1). Microbes have been characterized as “guardians of metabolism”, due to the fact that core genes of biogeochemical cycles are transferred among members of the community through horizontal gene transfer (1). Therefore, variety of different organisms in diverse environmental contexts can retain the genes of fundamental redox processes and protect the metabolic pathways even if the individual taxonomic unit goes extinct (1). An example of a biogeochemical flux that humans indirectly depend on, is the nitrogen cycle catalyzed by diverse, multispecies microbial interactions (1). Through nitrogen fixation by prokaryotes, the inert N2 atmospheric gas becomes accessible to plants in the form of NH4+ or NO3- for the synthesis of protein and nucleic acids (1,2). Plants then serve as a food source for humans and animals. Therefore, in the absence of microorganisms, primary production would be negatively impacted which further affect the terrestrial and oceanic food webs. Moreover, humans are directly dependent on the oxygen produced by microbes. Although higher plants are responsible for most of the photosynthesis carried out on land, the effect of terrestrial photosynthesis is minimal on atmospheric O2, because it is balanced by the reverse processes of respiration (3). Since only about 0.1% of the organic matter produced in oceans is buried in sediments, marine photosynthesis is mainly responsible for the atmospheric O2 (3). In fact, the majority of O2 that we breath is produced by photosynthetic bacteria in oceans such as prochlorococcus and Synechoccocus (4). Therefore, humans rely on the redox reactions catalysed by microbial communities, such as nitrogen fixation and marine photosynthesis for survival.
Secondly, microorganisms play an important role in making Earth a suitable place for living by reversing the negative effects of destructive human activities. A dramatic increase in atmospheric CO2 concentration has been observed due to the human activities such as combustion of fossil fuels and deforestation (5). Not only this increase in CO2 will lead to direct ecological disruption, but also it has the largest impact on the climate system (5). Eventually the elevation of temperature due to the increase in atmospheric CO2 combined with additional impacts of human activities such as pollution will make conditions on Earth intolerable for humans and animals and exceed the tolerance of ecosystem to adapt to increase in temperature (5). Although one can argue that humans might take an active role to engineer the climate and reverse the perturbation that they have caused in the first place. It should be noted that the process of “geoengineering”, if successful, is a slow process that might not meet the demands in time (5). On the other hand, microbes are constantly contributing to large fluxes of CO2 consumption. The major contributor to this negative flux is oxygenic photosynthetic cyanobacteria, which are believed to be responsible for the initial increase in atmospheric O2 about 2.3 billion years ago (3, 6). In oxygenic photosynthesis, Rubisco captures CO2 from the atmosphere-ocean, H2O act as an electron donor, and light is used and an energy source. Therefore, microorganism capture the solar energy, to convert greenhouse gases such as CO2 to sugars (7). It has been estimated that 10 billion tons of carbon is removed each year by Prochlorococcus and Synechococcus (8). Additional examples of pathways where microbes are involved in assimilation of CO2 into organic matter are reductive citric acid cycle and reductive acetyl-CoA pathway (1). Not only microbes are essential to reverse the greenhouse effect caused by humans, they can also degrade the pollution produced by destructive human activities. As an example, 1.3 million liters of crude oil (petroleum), which is composed of highly complex mixtures of organic compounds, enter the environment each year (9). The major contribution to the release of crude oil is illegal activities such the discharge of ballast water and oil residues in addition to oil spillage accidents (9). Examples of obligate hydrocarbon degraders include the genera Alcanivorax, Oleispira, and Cycloclasticus (9). These microorganisms play an important role in the degradation of oil in the ecosystem (9). Therefore, without microbes, waste management would be another problem that humans must deal with on top of greenhouse effect.
Lastly, prokaryotes have extremely large population size and rapid growth rate, which leads to higher mutation events and therefore immense capacity for genetic diversity (10). The number of prokaryotic cells on Earth is estimated to be around 4-6 x 10^30 cells (10).The genetic diversity has enabled prokaryotes to adapt to wide range of habitats, and even survive some of the harshest conditions such as hydrothermal vents (6). If conditions on Earth become unsuitable for humans, microbes can be selected for, adapt and survive and potentially change the composition of Earth’s atmosphere as they have been doing since the origin of life. Looking back over the history of Earth, about 3 billion years ago, the sun was much dimmer compared to now and therefore methanogen bacteria were contributing to greenhouse effect by producing CH4 which prevented Archean Earth from freezing and blocked UV light (3). About 2.4 billion years ago, microbes, specifically cyanobacteria, caused Earth great oxygenation event, which eventually lead to the presence of plants, animals and even humans on Earth (3). It should not be taken lightly, that microbes survived some of the harshest environmental conditions such as Snowball Earth, where the surface temperatures were bellow the freezing point and the planet was covered in deep sheet of ice (11). Therefore, if another such events are going to make Earth unsuitable for living, based on the evidence we have, microbes are going to be the only survivors.This is due to their rapid growth and turn over rates that allows for their significant genetic diversity.
In conclusion, not only are microbes contributing to the major biogeochemical cycles and metabolic pathways, they are also aiding humans in reversing the negative effects that they have caused by overexploitation of resources. I strongly believe that without microbes, the process of Earth becoming an uninhabitable place would accelerate in a much faster speed. However, due to their genetic diversity, microbes can adapt to different environments without depending on humans. Therefore, microbes are essential, and in order to save the Earth and its inhabitants dual intervention by microbes and humans is needed. This can be achieved through bioengineering of microbial communities using synthetically derived models, which allow for the greater understanding of ecological and environmental processes (12).
References
Falkowski PG, Fenchel T, Delong EF. 2008. The Microbial Engines That Drive Earths Biogeochemical Cycles. Science 320:1034-1039.(http://science.sciencemag.org/content/320/5879/1034.long)
Canfield DE, Glazer AN, Falkowski PG. 2010. The Evolution and Future of Earth’s Nitrogen Cycle. Science 330:192-196.(http://science.sciencemag.org/content/330/6001/192.long)
Kasting JF, Siefert JL. 2002. Life and the Evolution of Earth’s Atmosphere.Science 296:1066-1068.(http://science.sciencemag.org/content/296/5570/1066.long)
Gilbert JA, Neufeld JD. 2014. Life in a World without Microbes. PLoS Biology 12.(http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002020)
Schrag DP. 2012. Geobiology of the Anthropocene. Fundamentals of Geobiology 425-436.(https://onlinelibrary.wiley.com/doi/10.1002/9781118280874.ch22)
Nisbet EG, Sleep NH. 2001. The habitat and nature of early life. Nature 409:1083-1091.(https://www.nature.com/articles/35059210)
Donohue TJ, Cogdell RJ. 2006. Microorganisms and clean energy. Nature Reviews Microbiology 4: 800.(https://www.nature.com/articles/nrmicro1534)
Gupta C, Prakash D, Gupta S. Role of microbes in combating global warming. International Journal of Pharmaceutical Sciences Letters 4: 359-363.(https://www.researchgate.net/publication/264716464_Role_of_microbes_in_combating_global_warming)
Brooijmans RJW, Pastink MI, Siezen RJ. 2009. Hydrocarbon-degrading bacteria: the oil-spill clean-up crew. Microbial Biotechnology 2:587-594.PMC3815313
Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences 95:6578-6583. PMC33863
11.Hoffman, PF. 2016. Cryoconite Pans on Snowball Earth: Supraglacial Oases for Cryogenian Eukaryotes? Geobiology 14: 531–542. (http://advances.sciencemag.org/content/3/11/e1600983.full)
- Franks AE, and Sivasubramaniam D. 2016. Bioengineering microbial communities: Their potential to help, hinder and disgust. Bioengineered 7: 137-144. PMC4927200
Screen shots from marked module 1 essay
